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Cosegregation Analysis program help

Introduction.

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Leather Pull High Pumps Red WeenFashion Shoes Toe Patent Heels Closed Women's On We have developed an easy to use method which calculates the likelihood ratio (LR) of an unclassified variant in BRCA1 or BRCA2 to be deleterious. It requires only information on gender, genotype, present age and/or age of onset for breast and/or ovarian cancer. Although co-segregation analysis on itself is in most cases insufficient to prove pathogenicity of an UV, this method simplifies the use of co-segregation as one of the key features in a multifactorial approach considerably.

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A table is made based on the pedigree of the family.
Create a table with 10 columns (see below for example).
These columns respectively contain:

Leather Red Women's Toe High Shoes Patent Pull WeenFashion Closed On Heels Pumps SC6qwOP Leather Red Women's Toe High Shoes Patent Pull WeenFashion Closed On Heels Pumps SC6qwOP Leather Red Women's Toe High Shoes Patent Pull WeenFashion Closed On Heels Pumps SC6qwOP Leather Red Women's Toe High Shoes Patent Pull WeenFashion Closed On Heels Pumps SC6qwOP Leather Red Women's Toe High Shoes Patent Pull WeenFashion Closed On Heels Pumps SC6qwOP
  1. Person ID
  2. Father ID (0 if there is no father)
  3. Mother ID (0 if there is no mother)
  4. 1 for proband and 0 for others
  5. 12cm Pointed Out High Shoes Stiletto Elegante Women Cut Court Toe Heels Eldof Rose Leopard Pumps Classic vnFBxwqR1C
  6. On High Pumps Red Pull Shoes Leather Toe WeenFashion Heels Closed Women's Patent Current age (if ages are unknown, estimations can be made for each generation, based on the mean age of this generation)
  7. Gender (1=male, 2=female, 9=unknown)
  8. Age of onset of the first breast cancer (0 if there is no breast cancer)
  9. Age of onset of the second breast cancer (0 if there is no 2nd breast cancer)
  10. Age of onset of ovarian cancer (0 if there is no ovarian cancer)
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  12. Genotype (0 non-carrier, 1 carrier and 2 for unknown genotypes)

For an example look at figure 2 from the manuscript:

The corresponding matrix:

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Red Heels On Women's Leather Closed Toe Shoes Patent High Pull Pumps WeenFashion Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC WeenFashion Closed Women's Red Patent Pumps Heels Shoes High Leather Toe Pull On Age of onset OC Genotype
1 5 6 0 60 2 35 43 0 1
2 9 10 0 62 2 51 51 0 1
High Red Pumps Pull Toe Shoes Closed WeenFashion Leather Patent Heels On Women's 3 0 0 0 85 Women's WeenFashion On Patent Toe Shoes Leather Heels Closed Pumps High Red Pull 1 0 0 0 2
4 0 0 0 60 Patent Pumps WeenFashion On Shoes Women's Closed Pull High Toe Red Heels Leather 2 0 0 0 2
5 3 4 Women's Toe WeenFashion Heels Shoes On Patent Red Pumps High Closed Leather Pull 0 Pumps On Closed Leather Pull Patent Shoes Women's WeenFashion Toe Red High Heels 91 1 0 0 0 2
6 0 0 0 70 2 0 0 0 2
7 3 4 0 85 1 0 0 0 2
8 Patent High WeenFashion Pumps Leather Red Pull Toe Shoes On Women's Heels Closed 0 0 0 75 2 0 0 0 2
9 3 3 0 79 1 0 0 0 2
10 0 0 0 79 2 0 0 0 2
11 7 8 0 60 2 53 0 0 1
12 9 10 0 55 2 50 0 0 1
13 9 10 1 50 2 31 38 0 1

Copy the data (not the headings) from the matrix and paste them in simple text format, e.g. notepad.

Save the file as follows:

File name* FamilyID_BRCA1.ped or FamilyID_BRCA2.ped
Save as type All files
Encoding ANSI

*Use BRCA1 or BRCA2 depending on the gene in which the variant is located.

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Due to the difference in penetrance for mutations in BRCA1 and BRCA2, the gene in which the variant is located has to be selected for correct calculation of the LR.

Literature.

When using the analysis software, authors should refer to the following publication:

A simple method for co-segregation analysis to evaluate the pathogenicity of unclassified variants; Heels Pull Toe Closed On Shoes Women's WeenFashion Leather Patent Red Pumps High BRCA1 and BRCA2 as an example. Leila Mohammadi, Maaike P. Vreeswijk, Rogier Oldenburg, Ans van den Ouweland, Jan C. Oosterwijk, Annemarie H. van der Hout, Nicoline Hoogerbrugge, Marjolijn Ligtenberg, Margreet G.Ausems, Rob B. van der Luijt, Charlotte J. Dommering, Jan J.Gille, Senno Verhoef, Frans B. Hogervorst, Theo A.van Os, Encarna Gómez García, Marinus J. Blok, Juul Th. Wijnen, Peter Devilee, Christi J. van Asperen and Hans C. van Houwelingen. Submitted for publication.

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